In 1989, Yates tested positive for anabolic steroids in a doping test in the first stage of Torhout-Werchter.[4] However, his 'B' sample did not confirm the 'A' sample[5] and Yates was subsequently cleared because it was accepted that a labelling error must have occurred and the tested sample was not his.[6]

Following the report in October 2012 from the US Anti-Doping Agency that detailed organised doping in the US Postal/Discovery Channel teams, Yates insisted on BBC Radio 5 Live that he saw nothing suspicious during his six years working alongside Lance Armstrong.[7]

After retiring in 1996, Yates became manager of the Linda McCartney Racing Team, which competed at the Giro d'Italia. After the team's collapse in 2001, Yates helped set up the Australian iteamNova but left after funds ran out. After six months out of cycling, he joined Team CSC-Tiscali before moving to Discovery, in 2005, at the invitation of Lance Armstrong. In June 2007, Yates was manager of Team Discovery a USA team and, in 2008, went on to manage riders on the Astana cycling team.

In October 2012, he left the employment of Team Sky and retired from cycling,[9] with The Daily Telegraph reporting that Yates had been forced to quit after admitting involvement in doping, meaning he did not meet the team's zero tolerance stance on doping.[10] Both Sky and Yates denied that his exit was linked to the team's new requirement that all employees sign a declaration pledging no previous involvement in doping.[5]

After a year away from the sport, in October 2013 it emerged that Yates had agreed to take the position of directeur sportif for the NFTO team from the 2014 season.[11] Subsequently Yates clarified that this role would be limited to the first three rounds of the Premier Calendar and the Tour Series. He is also involved in coaching the Catford CC-Equipe Banks under-23 team, which includes his son Liam on its roster.[12] In November 2014 he was announced by Team Tinkoff-Saxo as one of their sports directors for the 2015 season.[13]

In 1997, he won the British 50-mile time-trial championship, and he finished third in the same event in 2005. In May 2007, he said he would not compete as a veteran because of heart irregularities, but he still competes at regional events, primarily in the Southeast. Yates currently plays football for Old St Marys Football Club as a goalkeeper in Amateur Football Combination.[14]